In cases like this, your reaction to the situation can make matters even worse than they are initially. Here is something we see pretty often. Something will happen and a dog will startle as a result (say a motorcycle came by). An owner pulled their dog to them and petted them and told them everything was ok and not to worry. The dog's brain sees attention as a reward for the fearful behavior. The next time the motorcycle comes by, the dog startles again and the owner agains repeats the attention. This is positive reinforcement for the unwanted behavior. Now we come to the part where each time a motorcycle comes by the owner anticipates the behavior and starts worrying about how the dog is going to react. The dog in turn picks up the owners fellings and then figures that if his owner is worried about the motorcycle then he should be as well which again reinforces the behavior.
I wanted to explain this scenario as your dog's problem may have started in a similar way. The best way of stopping this behavior is to provide positive reinforcement when he doesn't react to them. This also means that you will need to remain calm and not anticipate any particular reaction from your dog as well. I would use paper thin hot dog slices as these are smelly and dogs seem to love them and they are usually a good distraction for a dog.
You will want to train your dog to ignore the balloons. Start by sitting outside with your dog on a lead close to you. When you spot the baloons, order your dog to sit and then reward him with the hot dog slices. Your goal is to keep him occupied while the balloons pass over. As long as he is sitting and not bolting, reward him. Dogs are very food oriented and this may keep his mind off the balloons. Remember to keep the slices paper thing so he won't be eating too much hot dog. Practice this a couple of times a day. If he tries to bolt just hold the lead and ignore his behavior. Look at the baloon or the trees or do anything but pay attention to him. Once he is calm again, then you can pay him attention. It shouldn't take him more than a few times before he realizes that he is getting treats when the balloons are there. If you are consistant with the treats, he will start associating the balloons with hot dogs and will come to you when he sees the balloons eventually.
You might also try taking him to a place where the balloons are being launched. Seeing the balloons on the ground and going up may also help him get over his fear as well since they will no longer be an unknown item. Over time you should be able to cut down the number of treats substituting praise for good behavior and eventually do away with the treats all together.
Of course, if even training doesn't seem to have an effect, medication may need to be prescribed, but if the balloons are around several times a day, that would not be a good solution. I do hope my suggestions are helpful to you and your dog.